Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach

Genetics

Volumn 186, Issue 2, 2010, Pages 493-503

  Zanders, Sarah ^a   Ma, Xin ^b   RoyChoudhury, Arindam ^b,d   Hernandez, Ryan D ^c,e   Demogines, Ann ^a,f   Barker, Brandon ^a   Gu, Zhenglong ^a   Bustamante, Carlos D ^b,g   Alani, Eric ^a  

^a 459 Biotechnology Bldg ^*  (United States)

^b Program on Infrastructure Policy   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d Columbia University ^*  (United States)

^e University of California   (United States)

^f UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^g STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

ARTICLE; BAYES THEOREM; DIPLOIDY; DNA REPLICATION; FRAMESHIFT MUTATION; GENE DELETION; GENE FUNCTION; GENE INSERTION; GENE MUTATION; GENOME; GENOME ANALYSIS; GENOMICS; GENOTYPE; MISMATCH REPAIR; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SINGLE NUCLEOTIDE POLYMORPHISM; YEAST;

BASE SEQUENCE; BAYES THEOREM; CYTOGENETIC ANALYSIS; DATA INTERPRETATION, STATISTICAL; DNA MISMATCH REPAIR; DNA REPAIR; DNA REPLICATION; FRAMESHIFT MUTATION; GENOME, FUNGAL; HETEROZYGOTE; INDEL MUTATION; MUTAGENESIS, INSERTIONAL; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SACCHAROMYCES CEREVISIAE; SEQUENCE DELETION;

SACCHAROMYCES CEREVISIAE;

EID: 78951483949     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.120105     Document Type: Article

References (31)

1. ARNDT, P. F., T. HWA and D. A. PETROV, 2005 Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J. Mol. Evol. 60: 748-763.
2. DATTA, A., and S. JINKS-ROBERTSON, 1995 Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 268: 1616-1619.
3. DENVER, D. R., S. FEINBERG, S. ESTES, W. K. THOMAS and M. LYNCH, 2005 Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans. Genetics 170: 107-113.
4. DENVER, D. R., P. C. DOLAN, L. J. WILHELM, W. SUNG, J. I. LUCAS-LLEDÓ et al., 2009 A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proc. Natl. Acad. Sci. USA 106: 16310-16314.
5. DOHM, J. C., C. LOTTAZ, T. BORODINA and H. HIMMELBAUER, 2008 Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36: e105.
6. GIAEVER, G., A. M. CHU, L. NI, C. CONNELLY, L. RILES et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
7. GRAGG, H., B.D.HARFE and S. JINKS-ROBERTSON, 2002 Base composition of mononucleotide runs affects DNA polymerase slippage and removal of frameshift intermediates by mismatch repair in Saccharomyces cerevisiae. Mol. Cell. Biol. 22: 8756-8762.
8. HARDISON, R. C., K. M. ROSKIN, S. YANG, M. DIEKHANS, W. J. KENT et al, 2003 Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13: 13-26.
9. HARFE, B. D., and S. JINKS-ROBERTSON, 2000 Sequence composition and context effects on the generation and repair of frameshift intermediates in mononucleotide runs in Saccharomyces cerevisiae. Genetics 156: 571-578.
10. HAWK, J. D., L. STEFANOVIC, J. C. BOYER, T.D. PETES and R. A. FARBER, 2005 Variation in efficiency of DNA mismatch repair at diferent sites in the yeast genome. Proc. Natl. Acad. Sci. USA 102: 8639-8643.
11. HECK, J. A., D. GRESHAM, D. BOTSTEIN and E. ALANI, 2006 Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements. Genetics 174: 519-523.
12. IYER, R. R., A. PLUCIENNIK, V. BURDETT and P. L. MODRICH, 2006 DNA mismatch repair: functions and mechanisms. Chem. Rev. 106: 302-323.
13. KADYROV, F. A., L. DZANTIEV, N. CONSTANTIN and P. MODRICH, 2006 Endonucleolytic function of MutLalpha in human mismatch repair. Cell 126: 297-308.
14. KADYROV, F. A., S. F. HOLMES, M. E. ARANA, O. A. LUKIANOVA, M. O'DONNELL et al., 2007 Saccharomyces cerevisiae MutLalpha is a mismatch repair endonuclease. J. Biol. Chem. 282: 37181-37190.
15. KEIGHTLEY, P. D., U. TRIVEDI, M. THOMSON, F. OLIVER, S. KUMAR et al., 2009 Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res. 19: 1195-1201.
16. KUNKEL, T. A., and D. A. ERIE, 2005 DNA mismatch repair. Annu. Rev. Biochem. 74: 681-710.
17. LITI, G., D. M. CARTER, A. M MOSES, J. WARRINGER, L. PARTS, et al., 2009 Population genomics of domestic and wild yeasts. Nature 458: 337-341.
18. LYNCH, M. W., SUNG, K. MORRIS, N. COFFEY, C. R. LANDRY et al., 2008 A genome- wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl. Acad. Sci. USA 105: 9272-9277.
19. MARSISCHKY, G. T., N. FILOSI, M. F. KANE and R. KOLODNER, 1996 Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair. Genes Dev. 10: 407-420.
20. MATASSI, G., P. M. SHARP and C. GAUTIER, 1999 Chromosomal location effects on gene sequence evolution in mammals. Curr. Biol. 9: 786-791.
21. MCCULLOCH, S. D., and T. A. KUNKEL, 2008 The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res. 18: 148-161.
22. MODRICH, P., and R. S. LAHUE, 1996 Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Ann. Rev. Biochem. 65: 101-133.
23. NISHANT, K. T., N. D. SINGH and E. ALANI, 2009 Genomic mutation rates: what high-throughput methods can tell us. BioEssays 31: 912-920.
24. NISHANT, K. T., W. WEI, E. MANCERA, J. L. ARGUESO, A. SCHLATTL et al., 2010 The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. PLoS Genetics (in press).
25. STAMATOYANNOPOULOS, J. A., I. ADZHUBEI, R. E. THURMAN, G. V. KRYUKOV, S. M. MIRKIN et al., 2009 Human mutation rate associated with DNA replication timing. Nat. Genet. 41: 393-395.
26. TEYTELMAN, L, M. B. EISEN and J. RINE, 2008 Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts. PLoS Genet. 4: e1000247.
27. TRAN, H. T., J. D. KEEN, M. KRICKER, M. A. RESNICK and D. A. GORDENIN, 1997 Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants. Mol. Cell. Biol. 17: 2859-2865.
28. TRAN, P. T., J. A. SIMON and R. M. LISKAY, 2001 Interactions of Exo1p with components of MutLa in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 98: 9760-9765.
29. WASHIETL, S., R. MACHNÉ and N. GOLDMAN, 2008 Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 24: 583-587.
30. WEI, W., J. H. MCCUSKER, R. W. HYMAN, T. JONES, Y. NING et al., 2007 Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc. Natl. Acad. Sci. USA 104: 12825-12830.
31. WOLFE, K. H., P.M. SHARP and W. H. LI, 1989 Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.